Updates to analysis code in response to first round of reviews at Nature Neuroscience. Main additions:
- PAPA predicted PAS validation using poly(A)-tail containing reads
- Run DaPars2 using 3'Ext coordinates
- Analysis of ELK1 3'Ext RNA ribosome-association using Frac-seq data
- Isoform-specific SLAM-seq analysis
- Fixed FACS-seq analysis bug causing misassignment of cryptic APAs to event types (complete rewrite)
Minor:
- Improved documentation of workflow order and analysis scripts (actions, dependencies).
- Minor tidying up/reporting of scripts irrelevant to the main manuscript